Pluto Bioinformatics

GSE100495: Difference in characteristics between Endocardially-derived cardiac tissue macrophages (EcTMs) and non-Endocardially-derived cardiac tissue macrophages (non EcTMs)

Bulk RNA sequencing

[Purpose] To define the traditional profile of EcTMs, RNA seq analysis were parformed on EcTMs and non EcTMs at postnatal day28. [Method] The workflow consists of first-strand synthesis, template switching, adaptor ligation, cleavage of ribosomal cDNA and PCR amplification. Different adaptors were used for multiplexing samples in one lane. Sequencing was performed on an Illumina Nextseq500 a single read 75 run. Data quality check was conducted on Illumina SAV. Demultiplexing was performed with the Illumina Bcl2fastq2 v 2.17 program. Reads were aligned to the UCSC mm10 reference genome map using TopHat. DEseq2 was used to identify differentially expressed genes of EcTMs compared to non-EcTMs. 36 upregulated genes in EcTMs compared to non-EcTMs with a padj < 0.05 were subsequently clustered and visualized using R. Gene ontology functional analyses were performed using the database for annotation, visualization, and integrated discovery (DAVID) online tool.[Result] 40 genes were differentially expressed between the two groups: 36 were higher and 4 genes were lower in EcTMs compared to non-EcTMs. Gene Ontology analysis revealed that EcTMs were enriched for genes related to antigen presentation, lysosomes, and phagosomes (H2-Ab1, H2-Aa, H2-Eb1, CD74, Laptm5). [Conclusion] EcTMs would have higher potential for presenting antigen and phagositosis compared to non EcTMs. SOURCE: Ayako Shigeta (ayakosh@nifty.com) - UCLA